When I started the dlc, i was close to finishing the main quest-line, and had reputations with several factions. I managed to complete it relativly bug-free, but now everytime I return to the mojave, the game erases my reptuation with several main groups, like the legion, ncr, and bos. I'm not sure if anybody else has experienced this, but if anybody could help, it would be appriciated.

Are you wearing any faction armour?